def _run_cleanup_pipeline(args):
bam_cleanup = _build_wrapper_command(args)
procs = {}
try:
# Update 'procs' and get the last process in the pipeline
if args.paired_ended:
last_proc = _setup_paired_ended_pipeline(procs, bam_cleanup)
else:
last_proc = _setup_single_ended_pipeline(procs, bam_cleanup)
# Sort, output to stdout (-o)
call_sort = ['samtools', 'sort', "-o", "-", args.temp_prefix]
procs["sort"] = processes.open_proc(call_sort,
stdin=last_proc.stdout,
stdout=processes.PIPE,
close_fds=True)
last_proc.stdout.close()
# Update NM and MD tags; output BAM (-b) to stdout
call_calmd = ['samtools', 'calmd', '-b', '-', args.fasta]
procs["calmd"] = processes.open_proc(call_calmd,
stdin=procs["sort"].stdout)
procs["sort"].stdout.close()
if any(processes.join_procs(procs.values())):
return 1
return 0
except:
for proc in procs.itervalues():
proc.terminate()
raise
def _setup_paired_ended_pipeline(procs, bam_cleanup):
# Convert input to (uncompressed) BAM
procs["pipe"] = processes.open_proc(bam_cleanup + ["pipe"],
stdin=sys.stdin,
stdout=processes.PIPE,
close_fds=True)
sys.stdin.close()
# Fix mate information for PE reads
call_fixmate = ['samtools', 'fixmate', '-', '-']
procs["fixmate"] = processes.open_proc(call_fixmate,
stdin=procs["pipe"].stdout,
stdout=processes.PIPE,
close_fds=True)
procs["pipe"].stdout.close()
# Cleanup / filter reads. Must be done after 'fixmate', as BWA may produce
# hits where the mate-unmapped flag is incorrect, which 'fixmate' fixes.
procs["cleanup"] = processes.open_proc(bam_cleanup + ['cleanup'],
stdin=procs["fixmate"].stdout,
stdout=processes.PIPE,
close_fds=True)
procs["fixmate"].stdout.close()
return procs["cleanup"]
def _setup_paired_ended_pipeline(procs, bam_cleanup):
# Convert input to (uncompressed) BAM
procs["pipe"] = processes.open_proc(bam_cleanup + ["pipe"],
stdin=sys.stdin,
stdout=processes.PIPE,
close_fds=True)
sys.stdin.close()
# Fix mate information for PE reads
call_fixmate = ['samtools', 'fixmate', '-', '-']
procs["fixmate"] = processes.open_proc(call_fixmate,
stdin=procs["pipe"].stdout,
stdout=processes.PIPE,
close_fds=True)
procs["pipe"].stdout.close()
# Cleanup / filter reads. Must be done after 'fixmate', as BWA may produce
# hits where the mate-unmapped flag is incorrect, which 'fixmate' fixes.
procs["cleanup"] = processes.open_proc(bam_cleanup + ['cleanup'],
stdin=procs["fixmate"].stdout,
stdout=processes.PIPE,
close_fds=True)
procs["fixmate"].stdout.close()
return procs["cleanup"]
def _run_cleanup_pipeline(args):
bam_cleanup = _build_wrapper_command(args)
procs = {}
try:
# Update 'procs' and get the last process in the pipeline
if args.paired_ended:
last_proc = _setup_paired_ended_pipeline(procs, bam_cleanup)
else:
last_proc = _setup_single_ended_pipeline(procs, bam_cleanup)
# Sort, output to stdout (-o)
call_sort = ['samtools', 'sort', "-o", "-", args.temp_prefix]
procs["sort"] = processes.open_proc(call_sort,
stdin=last_proc.stdout,
stdout=processes.PIPE,
close_fds=True)
last_proc.stdout.close()
# Update NM and MD tags; output BAM (-b) to stdout
call_calmd = ['samtools', 'calmd', '-b', '-', args.fasta]
procs["calmd"] = processes.open_proc(call_calmd,
stdin=procs["sort"].stdout)
procs["sort"].stdout.close()
if any(processes.join_procs(procs.values())):
return 1
return 0
except:
for proc in procs.itervalues():
proc.terminate()
raise
def _create_genotyping_proc(setup):
mpileup_args = {"-u": None,
"-l": setup["files"]["bed"]}
mpileup_call = build_call(call=("samtools", "mpileup"),
args=mpileup_args,
new_args=args.mpileup_argument,
positional=("-",))
sys.stderr.write("Running 'samtools mpileup': %s\n"
% (" ".join(mpileup_call)))
procs = setup["procs"]
procs["mpileup"] \
= processes.open_proc(mpileup_call,
stdin=procs["filter"].stdout,
stdout=processes.PIPE,
close_fds=True)
bcftools_call = build_call(call=("bcftools", "view"),
args={},
new_args=args.bcftools_argument,
positional=("-",))
sys.stderr.write("Running 'bcftools call': %s\n"
% (" ".join(bcftools_call)))
procs["bcftools"] \
= processes.open_proc(bcftools_call,
stdin=procs["mpileup"].stdout,
stdout=processes.PIPE,
close_fds=True)
return procs["bcftools"].stdout
def setup_basic_batch(args, regions, prefix, func):
setup = {"files": {},
"temp_files": {},
"procs": {},
"handles": {}}
try:
setup["files"]["bed"] = write_bed_file(prefix, regions)
setup["temp_files"]["bed"] = setup["files"]["bed"]
filter_builder = factory.new("genotype")
filter_builder.set_option("--filter-only")
filter_builder.set_option("--bedfile", setup["files"]["bed"])
filter_builder.add_option(args.bamfile)
filter_builder.add_option(args.destination)
setup["procs"]["filter"] \
= processes.open_proc(filter_builder.call,
stdout=processes.PIPE,
close_fds=True)
setup["handles"]["outfile"] = open(prefix, "w")
zip_proc = processes.open_proc(["bgzip"],
stdin=func(setup),
stdout=setup["handles"]["outfile"],
close_fds=True)
setup["procs"]["gzip"] = zip_proc
return setup
except:
sys.stderr.write(traceback.format_exc() + "\n")
cleanup_batch(setup)
raise
def setup_basic_batch(args, regions, prefix, func):
setup = {"files": {}, "temp_files": {}, "procs": {}, "handles": {}}
try:
setup["files"]["bed"] = write_bed_file(prefix, regions)
setup["temp_files"]["bed"] = setup["files"]["bed"]
filter_builder = factory.new("genotype")
filter_builder.set_option("--filter-only")
filter_builder.set_option("--bedfile", setup["files"]["bed"])
filter_builder.add_option(args.bamfile)
filter_builder.add_option(args.destination)
setup["procs"]["filter"] = processes.open_proc(filter_builder.call, stdout=processes.PIPE, close_fds=True)
setup["handles"]["outfile"] = open(prefix, "w")
zip_proc = processes.open_proc(["bgzip"], stdin=func(setup), stdout=setup["handles"]["outfile"], close_fds=True)
setup["procs"]["gzip"] = zip_proc
return setup
except:
sys.stderr.write(traceback.format_exc() + "\n")
cleanup_batch(setup)
raise
def _setup_single_ended_pipeline(procs, bam_cleanup):
# Convert input to BAM and cleanup / filter reads
procs["pipe"] = processes.open_proc(bam_cleanup + ['cleanup-sam'],
stdin=sys.stdin,
stdout=processes.PIPE,
close_fds=True)
sys.stdin.close()
return procs["pipe"]
def _setup_single_ended_pipeline(procs, bam_cleanup):
# Convert input to BAM and cleanup / filter reads
procs["pipe"] = processes.open_proc(bam_cleanup + ['cleanup-sam'],
stdin=sys.stdin,
stdout=processes.PIPE,
close_fds=True)
sys.stdin.close()
return procs["pipe"]
def _create_mpileup_proc(setup):
mpileup_args = {"-l": setup["files"]["bed"]}
call = build_call(
call=("samtools", "mpileup"), args=mpileup_args, new_args=args.mpileup_argument, positional=("-",)
)
sys.stderr.write("Running 'samtools mpileup': %s\n" % (" ".join(call)))
procs = setup["procs"]
procs["mpileup"] = processes.open_proc(
call, stdin=procs["filter"].stdout, stdout=processes.PIPE, close_fds=True
)
return procs["mpileup"].stdout
def _create_genotyping_proc(setup):
mpileup_args = {"-u": None, "-l": setup["files"]["bed"]}
mpileup_call = build_call(
call=("samtools", "mpileup"), args=mpileup_args, new_args=args.mpileup_argument, positional=("-",)
)
sys.stderr.write("Running 'samtools mpileup': %s\n" % (" ".join(mpileup_call)))
procs = setup["procs"]
procs["mpileup"] = processes.open_proc(
mpileup_call, stdin=procs["filter"].stdout, stdout=processes.PIPE, close_fds=True
)
bcftools_call = build_call(
call=("bcftools", "view"), args={}, new_args=args.bcftools_argument, positional=("-",)
)
sys.stderr.write("Running 'bcftools call': %s\n" % (" ".join(bcftools_call)))
procs["bcftools"] = processes.open_proc(
bcftools_call, stdin=procs["mpileup"].stdout, stdout=processes.PIPE, close_fds=True
)
return procs["bcftools"].stdout
def _create_mpileup_proc(setup):
mpileup_args = {"-l": setup["files"]["bed"]}
call = build_call(call=("samtools", "mpileup"),
args=mpileup_args,
new_args=args.mpileup_argument,
positional=("-",))
sys.stderr.write("Running 'samtools mpileup': %s\n" % (" ".join(call)))
procs = setup["procs"]
procs["mpileup"] \
= processes.open_proc(call,
stdin=procs["filter"].stdout,
stdout=processes.PIPE,
close_fds=True)
return procs["mpileup"].stdout
